I noticed a wire connection under my hood. I don't know where it goes or if it was ever even connected. Any ideas

 

Post the link to your dropbox picture so we can see the pic.

 

right click it and open in another window

 

It's the connector between the engine harness and the Radio Noise Capacitor (bolted on the coil pack).

 

Does it need to be connected?

 

Yes, it should be if you can find a matching connector coming from the engine harness. Although the 99 Ford Wiring Diagrams manual shows the connector in the engine harness, some later 3.0's do not have it. So, if your engine harness or engine assembly have ever been replaced, there's a possibility that there is no matching connector.